Exactly.
Look at the dragons in 09. Bundled out in straight sets by 8th then 6th. Does anyone honestly think they deserved another shot at the premiership that year because they had to play 1 game away? They were the minor premiers, and if they believed themselves to be the premiers then they should have been able handle the broncos in brisbane, let along parramatta at Kogarah.
Similarly, look at Parramatta that same year. They went through 1st, 2nd and 3rd to get the the grand final, only to be defeated by 4th. Similar story with us in 2010 going through 2nd, 3rd and 4th in our run as well. If either side had taken out the title they'd have been worthy premiers.
Really the only times I'd say the old system was a bit iffy was the warriors in 2011 and the cowboys in 2005. Both were thumped in week one after finishing in the bottom of the 8, but were still given a 2nd chance and then went on a dream run to the GF (the cowboys were even allowed to move their semi to brisbane for some unknown reason that year). And really with the new system we are just as likely to see similarly "unfair" results from time to time as well.